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Data Standards

The HIPC data standards working group defines the metadata, assay results and controlled vocabularies used by HIPC centers to submit experimental results to NIAID/ImmPort. Most of the standards we develop are incorporated into the ImmPort data deposition templates. All HIPC centers submit data directly to ImmPort using the templates available on the ImmPort Website.

HIPC specifies content for some experiment types. This includes:

  • Transcription Profiling :

In addition to the experimental metadata submission to ImmPort, HIPC requires submission of the underlying data to NCBI. For details, please see HIPC Standards Working Group Transcription Profiling standards.

To download the ImmPort templates, click here.

Learn more on our forum page here.

  • Cell Cytometry Experiments :

HIPC defines the standard for specifying cell population definitions and names. For details, please see HIPC Standards Working Group Cell Population Specification.

In addition to raw data in .fcs files, HIPC requires the submission of derived data (e.g., the cell population frequencies). For CyTOF and flow cytometry, these are submitted using the associated derived data templates available below.

To download the ImmPort templates, click here.

Learn more on our forum page here.

  • Immune Exposure :

HIPC specifies a structured format (immune exposure model) to characterize human immune responses/mechanisms elicited by vaccinations, adjuvants or natural infection. For details, please see the following article: A structured model for immune exposures.

In addition, an immune exposure validator has been developed. The immune exposure metadata are entered using the human subject template available below.

To download the ImmPort templates, click here.

Learn more on our forum page here.

  • Mass Spectrometry-based Metabolomics, Proteomics and Lipidomics :

This HIPC data standard applies to mass spectrometry-based proteomics, metabolomics and lipidomics experimental data. For details, please see rules.

To download the ImmPort templates, click here.

Learn more on our forum page here.

  • Single cell RNA-seq :

This HIPC data standard applies to single cell transcriptional profiling data (including possible feature barcoding). It includes the submission of metadata to ImmPort with raw and processed data submitted to GEO and SRA. For more information, please see rules.

Learn more on our forum page here.

  • Multiplex Bead Array Assays (MBAA) (e.g. Luminex) :

In addition to results from the assayed biological samples (experimental samples), HIPC requires submission of the results from the control samples and their standard curves. These are submitted using the control sample and standard curve templates available on the ImmPort Website.

Learn more on our forum page here.

  • Hemagglutination Inhibition (HAI) Assay :

The virus strain names are validated using NCBI Taxon with links to Taxon IDs. HAI data are submitted using HAI results templates available on the ImmPort Website.

Learn more on our forum page here.

  • Human Subject

As part of the entry of the human subject’s demographic information, HIPC uses the Gazetteer ontology to standardize the country location with a link to the Gazetteer ID. For the United States, the location field also includes the name of the state. Location information is entered using the human subject template available on the ImmPort Website.

Publications

The following paper describes how to report and connect cell type names and gating definitions through ontologies including the Cell Ontology and Protein Ontology:

The following papers describe the development and use of a structured/ontological model to represent and validate human immune exposures elicited by vaccinations, adjuvants or natural infection:

Any questions ?

For questions about ImmPort data depositions, email: bisc_helpdesk@niaid.nih.gov

For questions about HIPC data standards, email: hipc-standards@googlegroups.com

More information about HIPC can be found here.